ZBTB39

zinc finger and BTB domain containing 39, the group of BTB domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 12:56998836-57006546

Links

ENSG00000166860 ∙ NCBI:9880 ∙ OMIM:619384 ∙ HGNC:29014 ∙ Uniprot:O15060 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZBTB39 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBTB39 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			55	2		57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	2	0

Variants in ZBTB39

This is a list of pathogenic ClinVar variants found in the ZBTB39 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-57002789-G-A		not specified	Uncertain significance (May 04, 2022)
12-57002826-T-G		ZBTB39-related condition	Uncertain significance (Apr 09, 2024)
12-57002852-G-C		not specified	Uncertain significance (Feb 26, 2024)
12-57002939-A-T		not specified	Uncertain significance (Jan 09, 2025)
12-57002951-G-A		not specified	Uncertain significance (Aug 08, 2022)
12-57002995-G-T		not specified	Uncertain significance (Nov 22, 2022)
12-57003003-G-A		not specified	Uncertain significance (Mar 04, 2024)
12-57003032-C-G		not specified	Uncertain significance (Jul 30, 2024)
12-57003066-T-C		not specified	Uncertain significance (Feb 17, 2022)
12-57003075-C-A		not specified	Uncertain significance (Oct 20, 2024)
12-57003128-T-C		not specified	Uncertain significance (Aug 23, 2021)
12-57003201-C-T		not specified	Uncertain significance (Oct 11, 2024)
12-57003226-A-C		not specified	Uncertain significance (Feb 14, 2025)
12-57003236-T-C		not specified	Uncertain significance (Feb 24, 2025)
12-57003254-T-G		not specified	Uncertain significance (Mar 31, 2023)
12-57003351-G-C		not specified	Uncertain significance (Oct 19, 2024)
12-57003383-A-G		not specified	Uncertain significance (Apr 19, 2023)
12-57003456-G-A		not specified	Uncertain significance (May 03, 2023)
12-57003506-A-G		not specified	Uncertain significance (Dec 19, 2023)
12-57003558-C-T		not specified	Uncertain significance (Jul 09, 2024)
12-57003582-C-T		not specified	Uncertain significance (Jan 03, 2022)
12-57003659-C-A		not specified	Uncertain significance (Jan 07, 2025)
12-57003659-C-T		not specified	Uncertain significance (Jun 07, 2024)
12-57003660-G-A		not specified	Uncertain significance (Feb 28, 2024)
12-57003662-C-T		not specified	Uncertain significance (May 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBTB39	protein_coding	protein_coding	ENST00000300101	1	7613

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000188	0.977	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0909	417	412	1.01	0.0000238	4760
Missense in Polyphen		206	225.99	0.91156		2616
Synonymous	-0.248	176	172	1.02	0.0000104	1407
Loss of Function	2.03	9	18.4	0.490	0.00000112	202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000167	0.000167
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.

Intolerance Scores

• loftool: 0.558
• rvis_EVS: -0.17
• rvis_percentile_EVS: 40.6

Haploinsufficiency Scores

• pHI: 0.395
• hipred: N
• hipred_score: 0.353
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.885

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Zbtb39

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding